Aquatic biotas of Sundaland and fragmented but not refugial

Tropical insular systems have long attracted biologists, stimulating some
important controversies in ecology and evolution. Eustatic fluctuations
during the Pleistocene have been invoked to explain species dispersal and
proliferation in these fragmented systems by controlling the extent of
landmasses and their temporary connections. In ancient archipelagos, the
Pleistocene represents only a small slice of their history so
long-standing configurations might better explain insular diversity
patterns. With a geological history of ca. 30 million years, the Sunda
Shelf is old. Upon entering the Pleistocene, islands of the Sunda Shelf
repeatedly separated and merged; however, recent reappraisals of its
paleoenvironments and evolutionary dynamics have questioned their
biogeographic significance. Based on the molecular inventory of six common
freshwater fish families, we explored population fragmentation and
demographic history of the most common species using mitochondrial DNA
sequences. Species delimitation methods, applied to 1,062 sequences
belonging to 37 species from 188 sites, detected 95 Molecular Operational
Taxonomic Units (MOTUs). Among the nine most widespread species, the
number of MOTUs ranged from 1 to 11 and correlated with time to the most
recent common ancestor. Extended Bayesian Skyline Plots applied to
mitogenomes and cytochrome c oxidase I sequence detected no variation in
past effective population size within MOTUs, while hierarchical
Approximate Bayesian Computation provided no evidence of congruent changes
in effective population sizes. Fragmentation of an ancestral range is the
most likely explanation for the rampant cryptic diversity observed, but
demographic inferences do not support MOTUs as being refugial from an
evolutionary perspective.